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Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits
Yang Wu1, Jian Zeng1, Futao Zhang1
1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
Nature Communications
|March 4, 2018
Summary
This study introduces a new method to identify genes and DNA methylation sites linked to complex traits and diseases. The findings reveal key regulatory elements and genes, offering insights into genetic disease mechanisms.
Area of Science:
- Genomics
- Epigenetics
- Complex Trait Genetics
Background:
- Genome-Wide Association Studies (GWAS) identify genetic variants associated with complex traits but require functional follow-up.
- Understanding the etiological basis of complex traits necessitates identifying the genes and regulatory elements influenced by GWAS loci.
Purpose of the Study:
- To develop an analytical framework for prioritizing genes and regulatory elements at GWAS loci for functional studies.
- To investigate the pleiotropic associations between DNA methylation sites, gene expression, and complex traits.
Main Methods:
- An integrative analysis combining summary-level SNP data from multi-omics studies.
- Detection of DNA methylation (DNAm) sites associated with gene expression and phenotype via shared genetic effects (pleiotropy).
- Association analyses linking methylome and transcriptome data to 12 complex traits.
Main Results:
- Identified 7858 DNAm sites and 2733 genes with pleiotropic associations.
- DNAm sites were enriched in enhancers and promoters, with over 40% mapping to distal genes.
- 149 DNAm sites and 66 genes were linked to 12 complex traits, suggesting a regulatory mechanism.
Conclusions:
- The developed analytical paradigm effectively prioritizes genes and regulatory elements for functional studies of GWAS loci.
- Pleiotropic associations between DNA methylation, gene expression, and complex traits highlight DNA methylation as a mediator of genetic effects on phenotype.
- This approach provides a mechanistic link between genetic variation, epigenetic regulation, and complex trait etiology.
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